AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00290_hpyl_reg_100.orf -o00290_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HP0330 248 ketol-acid reductoisomerase (ilvC) #2 HP1153 130 valyl-tRNA synthetase (valS) #3 HP1422 24 isoleucyl-tRNA synthetase (ileS) #4 HP1423 101 conserved hypothetical protein #5 HP1468 51 branched-chain-amino-acid aminotransferase (ilvE) #6 HP1469 114 H. pylori predicted coding region HP1469 #7 HP1550 62 protein-export membrane protein (secD) #8 HP1551 47 conserved hypothetical secreted protein #9 HP1552 23 Na+/H+ antiporter (nhaA) #10 HP1553 248 helicase Motif number 1 AGCTAATTTTTCACTTAAACGATGCGTTTTT 1 29 0 TCCTTAAACG 0.915178 -220 ATCGTTTCACTTCTTTAAAAGTGCTCGTAGC 1 75 1 TTTTTAAAAG 0.754453 -174 GAGCACACCATTTCTTAATATTCTGCATGTT 1 162 1 TTCTTAATAT 0.777071 -87 AAATAAATACTTGCTTAAACACGCTAGGAGA 1 221 1 TTCTTAAACA 0.933738 -28 AAATAGAGCGTTCCTTAAAAAATGGTTGGAT 2 100 0 TTCTTAAAAA 0.968907 -31 TATTATCCTAAAATAGAGCGTTCC 2 117 0 TACCTAAAAT 0.932224 -14 ACAAATTCCTTAAAAAGAGTGGTGGC 4 6 1 TTCTTAAAAA 0.968907 -96 TTTTTATCCATAACTTATAAGGGTTTTAGTT 4 55 0 TACTTATAAG 0.868366 -47 GGCGTGATTGTATCTAAAAAGGGG 5 4 0 TACTAAAAAG 0.77957 -48 TAATATATTTTTTCTTAAACTCAATTAAAAA 6 12 0 TTCTTAAACT 0.950972 -103 TGGCTAAGTATTACTTATAAAGAAATAATAA 6 40 0 TTCTTATAAA 0.808087 -75 TATATTATATTAGCTTAAAATGGCTAAGTAT 6 60 0 TACTTAAAAT 0.968557 -55 AGAAAACCCTACCCCTAAAAGAAGCGCGCCA 7 42 0 ACCCTAAAAG 0.590137 -21 TTAATTTCCTTAAAAGATGTTTTAAT 8 32 0 TTCTTAAAAG 0.985853 -16 AGACAACCTTAAAATTTTTAATT 9 9 0 AACTTAAAAT 0.80433 -15 GATTCTTAATTTTCTTAAGAACACCTAATAC 10 59 1 TTCTTAAGAA 0.872085 -190 AAAGCCTTTTTTACTTAAGCTAAAAAACCTT 10 184 0 TTCTTAAGCT 0.809522 -65 GTCTTTATTATAACCTAAAAGCCTTTTTTAC 10 201 0 TACCTAAAAG 0.95666 -48 TGAGATCTATCCTAAAATTCTAATTTTG 10 231 0 TACCTAAAAT 0.932224 -18 ** ******** Masking position 7 Map Score: 24.1158 Number of sites scoring better than the average of aligned sites = 730 Number in coding regions = 557 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 2 GCCTTAAATTATAATAGAAAAAACGCATCGTT 1 8 1 AATAAGAAAA 0.983809 -241 AAGTGAAACGATGATTATAGCAAGAAAAGCTAATT 1 52 0 AATAAGAAGA 0.919631 -197 CATTATCGCTCCCATTATGGTAAAATAAATACTTG 1 199 1 CATAGGAAAA 0.95607 -50 GCTTTGTTGTATAATTTTGAAAAAATACGCAACAA 2 35 1 AATTGAAAAA 0.693461 -96 AACAATTAAAAGCGTAAAAGCAAAAGGCGTTCCAA 2 65 1 AGTAAGAAAA 0.919631 -66 TAAAAACTTAAAGAATAGGGTAAAATAAACGC 4 80 1 AAAAGGAAAA 0.966301 -22 CGATTATCAAAAAATAAAGGGAAAAGACTGA 6 94 1 AATAGGAAAA 0.991421 -21 TCATTTTAATAGGAACAAGGCAAAGACAGCGTCAA 10 110 0 AAAAGGAAAG 0.84375 -139 TGTTCCTATTAAAATGATAGAAAAACGACAAAACC 10 128 1 AATAAGAAAA 0.983809 -121 ACAAAACCCTACGATTATAGCAAAAGATTAAGGTT 10 155 1 AATAAGAAAA 0.983809 -94 CTTTTAGGTTATAATAAAGACAAAATTAGAATTTT 10 211 1 AATAGAAAAA 0.946821 -38 * ** * ** **** Masking position 12 Map Score: 13.2113 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 167 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 3 CTTAAATTATAATAGAAAAAACGCATCGTT 1 13 1 AATAGAAAAA 0.81111 -236 CGCATCGTTTAAGTGAAAAATTAGCTTTTC 1 34 1 AAGTGAAAAA 0.811175 -215 ACTTTTAAAGAAGTGAAACGATGATTATAG 1 67 0 AAGTGAAACG 0.7768 -182 ATTATGGTAAAATAAATACTTGCTTAAACA 1 212 1 AATAAATACT 0.718931 -37 AAAGCATTTAAATTAAAAAGGATAGTCCA 2 10 0 AATTAAAAAG 0.869604 -121 ATAAGTTATGGATAAAAACTTAAAGAATAG 4 68 1 GATAAAAACT 0.77578 -34 TCTTAAACTCAATTAAAAAA 6 1 0 AATTAAAAAA 0.903535 -114 AATTGAGTTTAAGAAAAAATATATTATTAT 6 17 1 AAGAAAAAAT 0.881875 -98 ATTACTTATAAAGAAATAATAATATATTTT 6 32 0 AAGAAATAAT 0.667486 -83 ATTTCTTTATAAGTAATACTTAGCCATTTT 6 45 1 AAGTAATACT 0.719017 -70 GAAGCGCGCCAATAAAAACGATTAAACGAG 7 23 0 AATAAAAACG 0.871351 -40 TATAATTTGAGATTAAAACATCTTTTAAGG 8 21 1 GATTAAAACA 0.794925 -27 AATTAAAAATTTTAAGGTTG 9 1 1 AATTAAAAAT 0.903533 -23 TTCTTAAGAAAATTAAGAATCAAATGAGCA 10 50 0 AATTAAGAAT 0.731093 -199 CTATTAAAATGATAGAAAAACGACAAAACC 10 133 1 GATAGAAAAA 0.609652 -116 TTTTTAGCTTAAGTAAAAAAGGCTTTTAGG 10 189 1 AAGTAAAAAA 0.893208 -60 TTTAGGTTATAATAAAGACAAAATTAGAAT 10 213 1 AATAAAGACA 0.734128 -36 ********** Masking position 6 Map Score: 12.9214 Number of sites scoring better than the average of aligned sites = 1102 Number in coding regions = 908 Number in noncoding regions = 194 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 4 AATCAAATCTCCTAGCGTGTTTAAGCAAGTA 1 228 0 TTTAGCGTTT 0.889738 -21 TTACGCTTTTAATTGTTGCGTATTTTTTCAAAAT 2 48 0 ATTTGCGTTT 0.940325 -83 TTCCTTAAAAAATGGTTGGATTTGGAACGCCTTT 2 87 0 ATTTGGATTG 0.726031 -44 TAAGGGTTTTAGTTTTAGCATGTTAGCATTCAGC 4 35 0 ATTAGCATTT 0.958903 -67 TTTATCCATAACTTATAAGGGTTTTAGTTTTAGC 4 50 0 ATTAAGGGTT 0.77941 -52 CGCTTCTTTTAGGGGTAGGGTTTTCT 7 47 1 AGTAGGGTTT 0.979356 -16 TTTAATCTCAAATTATAGCATTTTTAG 8 4 0 ATTAGCATTT 0.958903 -44 AATTAAAAATTTTAAGGTTGTCT 9 8 1 ATTAAGGTGT 0.77941 -16 ACCTAATACAAGGATTAGCATGTGTGAATTTGAC 10 81 1 AGTAGCATTG 0.848685 -168 CTTTTGCTATAATCGTAGGGTTTTGTCGTTTTTC 10 147 0 ATTAGGGTTT 0.98697 -102 ATTATAGCAAAAGATTAAGGTTTTTTAGCTTAAG 10 168 1 AGTAAGGTTT 0.921571 -81 * * ****** ** Masking position 6 Map Score: 5.19709 Number of sites scoring better than the average of aligned sites = 1000 Number in coding regions = 867 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 5 AGTGAAAAATTAGCTTTTCTTGCTATAATC 1 45 1 TAGCTTTTCT 0.914417 -204 TTTTAGGGGTAGGGTTTTCT 7 53 1 AGGGTTTTCT 0.986316 -10 TAAAAATTTTAAGGTTGTCT 9 14 1 AAGGTTGTCT 0.969503 -10 ATCCTTGTATTAGGTGTTCTTAAGAAAATT 10 66 0 TAGGTGTTCT 0.944563 -183 CTATAATCGTAGGGTTTTGTCGTTTTTCTA 10 145 0 AGGGTTTTGT 0.953426 -104 GCAAAAGATTAAGGTTTTTTAGCTTAAGTA 10 174 1 AAGGTTTTTT 0.943376 -75 ********** Masking position 5 Map Score: 2.38645 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 110 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 ATAATAGAAAAAACGCATCGTTTAAGTGAAAA 1 21 1 AAACATCGTT 0.966773 -228 TTTTCTTGCTATAATCATCGTTTCACTTCTTT 1 59 1 ATACATCGTT 0.901907 -190 ATTTTACCATAATGGGAGCGATAATGTTTAAA 1 193 0 AATGAGCGAT 0.846761 -56 ATTTAAATTAAAAAGGATAGTCCA 2 3 0 AAAGATAGTC 0.844582 -128 TATTATCCTAAAATAGAGCGTTCCTTAAAAAA 2 109 0 AAAGAGCGTT 0.991057 -22 TCACACCTTTAAATGGATAGTTTCAGGCGTGA 5 28 0 AAAGATAGTT 0.917474 -24 AGCTAATATAATATAGAGCGATTATCAAAAAA 6 76 1 ATAGAGCGAT 0.917196 -39 TAAAAACGATTAAACGAGCGTTAAAAAGTT 7 9 0 TAAGAGCGTT 0.945906 -54 GGAACAAGGCAAAGACAGCGTCAAATTCACAC 10 102 0 AAACAGCGTC 0.965447 -147 *** ******* Masking position 7 Map Score: 6.13535 Number of sites scoring better than the average of aligned sites = 922 Number in coding regions = 841 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 7 ********** No masking Map Score: 2.11274e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 ********** No masking Map Score: 2.11274e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 9 ********** No masking Map Score: 2.11274e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0